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pipeline-tests.yml
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name: DeepRVAT Pipeline Tests
run-name: DeepRVAT Pipeline Tests 🧬🧪💻🧑🔬
on: [ push ]
jobs:
# Config Setup
Smoke-GenerateConfig-Training:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/run_training.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./example/config/deeprvat_input_training_config.yaml ./example/
Smoke-GenerateConfig-Training-AssociationTesting:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/training_association_testing.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./example/config/deeprvat_input_config.yaml ./example/
Smoke-GenerateConfig-PreTrained:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/association_testing_pretrained.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./example/config/deeprvat_input_pretrained_models_config.yaml ./example/ && ln -s $GITHUB_WORKSPACE/pretrained_models ./example/
# Training Pipeline
Smoke-RunTraining:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/run_training.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
Pipeline-Tests-RunTraining:
needs: [Smoke-RunTraining, Reference-Output-Training]
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/run_training.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
dry_run: false
download_training_outputs: true
run_training_results_check: true
Reference-Output-Training:
uses: ./.github/workflows/run-pipeline.yml
with:
branch: main
pipeline_file: ./pipelines/run_training.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
dry_run: false
upload_training_outputs: true
Reference-Output-Pretrained:
uses: ./.github/workflows/run-pipeline.yml
with:
branch: main
pipeline_file: ./pipelines/association_testing_pretrained.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/
dry_run: false
upload_pretrained_outputs: true
Reference-Output-Pretrained-Regenie:
uses: ./.github/workflows/run-pipeline.yml
with:
branch: main
pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/
dry_run: false
upload_regenie_outputs: true
# Association Testing Pretrained Pipeline
Smoke-Association-Testing-Pretrained:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/association_testing_pretrained.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/
Pipeline-Tests-Training-Association-Testing:
needs: [Smoke-Association-Testing-Pretrained, Reference-Output-Pretrained]
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/association_testing_pretrained.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/
dry_run: false
download_pretrained_outputs: true
run_burden_results_check: true
run_association_results_check: true
# Association Testing Pretrained Regenie
Smoke-Association-Testing-Pretrained-Regenie:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/
Pipeline-Tests-Association-Testing-Pretrained-Regenie:
needs: [Smoke-Association-Testing-Pretrained-Regenie, Reference-Output-Pretrained-Regenie]
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/
dry_run: false
download_regenie_outputs: true
#run_burden_results_check: true
run_regenie_association_results_check: true
# Association Testing Training
Smoke-Association-Testing-Training:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/training_association_testing.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
Pipeline-Tests-Association-Testing-Training:
needs: Smoke-Association-Testing-Training
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/training_association_testing.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/
dry_run: false
# Association Testing Training Regenie
Smoke-Association-Testing-Training-Regenie:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/training_association_testing_regenie.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/regenie/training_association_testing/deeprvat_config.yaml ./example/
Pipeline-Tests-Training-Association-Testing-Regenie:
needs: Smoke-Association-Testing-Training-Regenie
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/training_association_testing_regenie.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/deeprvat/regenie/training_association_testing/deeprvat_config.yaml ./example/
dry_run: false
# Seed Gene Discovery
Smoke-Seed-Gene-Discovery:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/seed_gene_discovery.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/seed_gene_discovery/sg_discovery_config.yaml ./example/
Pipeline-Tests-Seed-Gene-Discovery:
needs: Smoke-Seed-Gene-Discovery
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/seed_gene_discovery.snakefile
environment_file: ./deeprvat_env_no_gpu.yml
prerun_cmd: cp ./tests/seed_gene_discovery/sg_discovery_config.yaml ./example/
dry_run: false
# Preprocessing With QC
Smoke-Preprocessing-With-QC:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/preprocess_with_qc.snakefile
environment_file: ./deeprvat_preprocessing_env.yml
pipeline_directory: ./example/preprocess
pipeline_config: ./example/config/deeprvat_preprocess_config.yaml
download_fasta_data: true
fasta_download_path: ./example/preprocess/workdir/reference
Pipeline-Tests-Preprocessing-With-QC:
needs: Smoke-Preprocessing-With-QC
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/preprocess_with_qc.snakefile
environment_file: ./deeprvat_preprocessing_env.yml
pipeline_directory: ./example/preprocess
pipeline_config: ./example/config/deeprvat_preprocess_config.yaml
dry_run: false
download_fasta_data: true
fasta_download_path: ./example/preprocess/workdir/reference
# Preprocessing-No-QC
Smoke-Preprocessing-No-QC:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/preprocess_no_qc.snakefile
environment_file: ./deeprvat_preprocessing_env.yml
pipeline_directory: ./example/preprocess
pipeline_config: ./example/config/deeprvat_preprocess_config.yaml
download_fasta_data: true
fasta_download_path: ./example/preprocess/workdir/reference
Pipeline-Tests-Preprocessing-No-QC:
needs: Smoke-Preprocessing-No-QC
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/preprocess_no_qc.snakefile
environment_file: ./deeprvat_preprocessing_env.yml
pipeline_directory: ./example/preprocess
pipeline_config: ./example/config/deeprvat_preprocess_config.yaml
dry_run: false
download_fasta_data: true
fasta_download_path: ./example/preprocess/workdir/reference
# Annotation Pipeline
Smoke-Annotation-Pipeline:
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/annotations.snakefile
environment_file: ./deeprvat_annotations.yml
prerun_cmd: |
mkdir -pv ./example/preprocess/workdir/norm/variants && \
mkdir -pv ./example/preprocess/workdir/preprocessed && \
touch ./example/preprocess/workdir/preprocessed/genotypes.h5 && \
touch ./example/preprocess/workdir/norm/variants/variants.parquet
pipeline_config: ./example/config/deeprvat_annotation_config.yaml
pipeline_directory: ./example/annotations
download_fasta_data: true
fasta_download_path: ./example/annotations/reference
Pipeline-Annotation:
needs: Smoke-Annotation-Pipeline
uses: ./.github/workflows/run-pipeline.yml
with:
pipeline_file: ./pipelines/annotations.snakefile
environment_file: ./deeprvat_annotations.yml
prerun_cmd: |
mkdir ./example/annotations/repo_dir && \
bash deeprvat/annotations/setup_annotation_workflow.sh ./example/annotations/repo_dir faatpipe && \
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.annotation.gtf.gz \
-O ./example/annotations/reference/gencode.v44.annotation.gtf.gz
pipeline_directory: ./example/annotations
pipeline_config: ./example/config/deeprvat_annotation_config_minimal.yaml
dry_run: false
download_fasta_data: true
fasta_download_path: ./example/annotations/reference